Distance conservation of transcription regulatory motifs in human promoters

Computational Biology and Chemistry
Jun LuYing Zhang

Abstract

To understanding the interaction network among transcription-regulation elements in human is an immediate challenge for modern molecular biology. Here a central problem is how to extract evolutionary information and search the evolutionary conservation from the comparison of promoters of closely related species. Through the comparative studies of k-mer distribution in human and mouse transcription factor binding site (TFBS) sequences we have discovered that the average distance between a pair of transcription regulatory 7-mer motifs is conservative in human-mouse promoters. The distance conservation is a new kind of evolutionary conservation, not based on the strict location of bases in genome sequence. By utilizing the conservation of k-mer distance it will be helpful to propose a non-alignment-based approach for fast genome-wide discovery of transcription regulatory motifs. We demonstrated the distance conservation by genome-wide searching of conservative regulatory 7-mer motifs with successful rate 90%. Then, after defining human-mouse pair-distance divergence parameter we studied the tissue-specific motif pairs and found that the parameter for motif pairs is 11-16 times smaller than for their controls for 28 tissues and the...Continue Reading

References

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Oct 25, 2003·Nucleic Acids Research·Lirong Zhang, Liaofu Luo
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Citations

Oct 7, 2009·Proceedings of the National Academy of Sciences of the United States of America·Gregory E SimsSung-Hou Kim
Jan 15, 2016·Scientific Reports·Hideaki Abe, Neil J Gemmell

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